Sequence analysis and gene expression of putative oil palm chitinase and chitinase-like proteins in response to colonization of Ganoderma boninense and Trichoderma harzianum

Chitinases are glycosyl hydrolases that cleave the β-1,4-glycosidic linkages between N-acetylglucosamine residues in chitin which is a major component of fungal cell wall. Plant chitinases hydrolyze fungal chitin to chitin oligosaccharides that serve as elicitors of plant defense system against fungal pathogens. However, plants synthesize many chitinase isozymes and some of them are not pathogenesis-related. In this study, three full-length cDNA sequences encoding a putative chitinase (EgChit3-1) and two chitinase-like proteins (EgChit1-1 and EgChit5-1) have been cloned from oil palm (Elaeis guineensis) by polymerase chain reaction (PCR). The abundance of these transcripts in the roots and leaves of oil palm seedlings treated with Ganoderma boninense (a fungal pathogen) or Trichoderma harzianum (an avirulent symbiont), and a combination of both fungi at 3, 6 and 12 weeks post infection were profiled by real time quantitative reverse-transcription (qRT)-PCR. Our findings showed that the gene expression of EgChit3-1 increased significantly in the roots of oil palm seedlings treated with either G. boninense or T. harzianum and a combination of both; whereas the gene expression of EgChit1-1 in the treated roots of oil palm seedlings was not significantly higher compared to those of the untreated oil palm roots. The gene expression of EgChit5-1 was only higher in the roots of oil palm seedlings treated with T. harzianum compared to those of the untreated oil palm roots. In addition, the gene expression of EgChit1-1 and EgChit3-1 showed a significantly higher gene expression in the leaf samples of oil palm seedlings treated with either G. boninense or T. harzianum

Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis.

Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was insignificant. A deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had increased the number of identified proteins from oil palm mesocarps, enriched their gene ontologies and reduced the number of carbamylated lysine residues by more than 67.0%, compared to urea/thiourea/CHAPS buffer. Although only 62.0% of the total identified proteins were shared between the urea/thiourea/CHAPS and sodium deoxycholate buffers, the importance of the remaining 38.0% proteins depends on the applications. The only observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and but it could be easily rectified through a 4-fold dilution. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps with higher efficiency compared to urea/thiourea/CHAPS buffer. The sodium deoxycholate buffer is more favorable for proteomics analysis due to its proven advantages over urea/thiourea/CHAPS buffer

Correlation between non-robosomal peptide synthetase (NRPS) production and virulence of Ganoderma boninense PER71 on oil palm (Elaeis guineensis)

Basal stem rot (BSR) disease caused by the white rot fungus Ganoderma boninense is the most destructive oil palm disease leading to production losses in fresh fruit bunches. Non-ribosomal peptide synthetase (NRPS) plays an important role in fungal pathogenicity. These large multi-modular enzymes catalyse the biosynthesis of secondary metabolites that act as fungal virulence factors. In this study, the detection of NRPS in G. boninense was achieved using polymerase chain reaction (PCR)-based method. Core motifs of adenylation domain of NRPS gene was identified in G. boninense. The deduced amino acid sequence showed similarity to the conserved core motifs (A2, A3 and A5) of the adenylation domain. Siderophores were predicted as the potential secondary metabolites synthesised by NRPS. Expression analysis of GbNRPS in 3-month-old oil palm artificially infected with G. boninense has confirmed the upregulation of GbNRPS at 1 month after inoculation (MAI) peaking at 4 MAI in susceptible clone but not in tolerant clone. There was a correlation between GbNRPS gene expression and disease severity. Susceptible clones showed significantly higher disease severity index (DSI) (62.50%) compared to tolerant clones (28.13%) at 4 MAI. This is the first putative detection of adenylation domain of NRPS (GbNRPS) gene and functional analysis of NRPS as a virulence factor in disease development

Use of headspace–gas chromatography–ion mobility spectrometry to detect volatile fingerprints of palm fibre oil and sludge palm oil in samples of crude palm oil

Abstract Objective The addition of residual oils such as palm fibre oil (PFO) and sludge palm oil (SPO) to crude palm oil (CPO) can be problematic within supply chains. PFO is thought to aggravate the accumulation of monochloropropanediols (MCPDs) in CPO, whilst SPO is an acidic by-product of CPO milling and is not fit for human consumption. Traditional targeted techniques to detect such additives are costly, time-consuming and require highly trained operators. Therefore, we seek to assess the use of gas chromatography–ion mobility spectrometry (GC–IMS) for rapid, cost-effective screening of CPO for the presence of characteristic PFO and SPO volatile organic compound (VOC) fingerprints. Results Lab-pressed CPO and commercial dispatch tank (DT) CPO were spiked with PFO and SPO, respectively. Both additives were detectable at concentrations of 1% and 10% (w/w) in spiked lab-pressed CPO, via seven PFO-associated VOCs and 21 SPO-associated VOCs. DT controls could not be distinguished from PFO-spiked DT CPO, suggesting these samples may have already contained low levels of PFO. DT controls were free of SPO. SPO was detected in all SPO-spiked dispatch tank samples by all 21 of the previously distinguished VOCs and had a significant fingerprint consisting of four spectral regions

Sustainable Palm Oil—The Role of Screening and Advanced Analytical Techniques for Geographical Traceability and Authenticity Verification

Palm oil production from oil palm (Elaeis guineensis Jacq.) is vital for the economy of Malaysia. As of late, sustainable production of palm oil has been a key focus due to demand by consumer groups, and important progress has been made in establishing standards that promote good agricultural practices that minimize impact on the environment. In line with the industrial goal to build a traceable supply chain, several measures have been implemented to ensure that traceability can be monitored. Although the palm oil supply chain can be highly complex, and achieving full traceability is not an easy task, the industry has to be proactive in developing improved systems that support the existing methods, which rely on recorded information in the supply chain. The Malaysian Palm Oil Board (MPOB) as the custodian of the palm oil industry in Malaysia has taken the initiative to assess and develop technologies that can ensure authenticity and traceability of palm oil in the major supply chains from the point of harvesting all the way to key downstream applications. This review describes the underlying framework related to palm oil geographical traceability using various state-of-the-art analytical techniques, which are also being explored to address adulteration in the global palm oil supply chain